LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT


neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles

compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTs
  3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50    1.1419601    6863.6417    4633.9267    321.70512     2229.715     735.2547    604.69459    648.35773    49.039129    824.06033    1306091.3   -1306722.9    17914.827    48631.318    504.18525 0.0086839775 
     100    2.3001912    6628.0719    4376.1868    303.81182    2251.8851    598.11248    651.43051    919.41359    74.216825     589.6504    1306135.1     -1306716    17450.721    48631.318    476.14276 0.0075129701 
     150     3.473469    6336.1884    4726.0692    328.10201    1610.1192    560.01225    621.30109    640.32474    45.531174    288.99129    1306173.9     -1306720    18303.624    48631.318    514.21215  0.006192153 
     200    4.6296241    5997.6192    4565.6288    316.96362    1431.9903    524.27651    591.79844    718.11014    56.374557     88.66084      1306183   -1306730.3    17986.183    48631.318    496.75522 0.0068120542 
     250    5.7982912    5648.1756    4433.1557    307.76682    1215.0199    502.13686     578.8537    665.27326    49.096119   -19.019961    1306179.2   -1306740.5    11771.328    48631.318    482.34141 0.0071619522 
     300    6.9468622    5317.8583    4075.2077    282.91669    1242.6505    602.55113    637.40818    647.27073    44.769725   -123.22347    1306183.3   -1306749.5    3571.1872    48631.318     443.3952 0.0071733908 
     350    8.0925181    4996.7094    3935.7988    273.23838    1060.9106    455.75195     634.3655    638.77824    45.831051   -157.63039    1306198.1   -1306754.3    13525.265    48631.318    428.22739 0.0063722017 
     400    9.2309761    4695.9294    3742.6584    259.82983    953.27093    457.49585    620.73048    591.94413    42.495714   -183.91838    1306186.7   -1306762.2    10901.217    48631.318    407.21326    0.0057875 
     450    10.363872    4417.8018    3513.6374     243.9303     904.1644    519.61261    580.76003    624.06933    45.631272   -286.60025    1306184.3   -1306763.6    2956.9021    48631.318    382.29485 0.0057536673 
     500    11.493601    4165.0005    3333.7203    231.43976    831.28022    465.52341    579.36085    580.60004    42.345149   -254.82269    1306183.9   -1306765.6    5818.5549    48631.318    362.71904 0.0059224858 
     550    12.636785    3934.5207    3211.9362    222.98504    722.58446    431.14864    581.46511    517.20249    39.188194    -265.4704    1306182.7   -1306763.6    8537.9415    48631.318    349.46863 0.0055762027 
     600    13.759642    3714.8658    3121.0493    216.67532    593.81649    425.12998    539.89497    490.30506    34.564567   -305.82067    1306175.2   -1306765.5    7402.7688    48631.318    339.57967  0.005748668 
     650    14.880794    3516.2453    2930.7499      203.464    585.49542    511.91457    512.48857    521.40634    37.766798   -391.65394    1306163.5     -1306770    381.72898    48631.318    318.87448 0.0054629381 
     700     15.99791    3342.7693    2864.1576     198.8409    478.61174    451.54685    498.82406    489.17206    35.231269   -375.78888    1306153.8   -1306774.2    3691.2706    48631.318    311.62801 0.0071278792 
     750    17.111346    3181.7665    2786.7104    193.46422    395.05608    409.83191    508.19537    454.56183    32.890719   -379.80694      1306149   -1306779.6    7428.3698    48631.318    303.20196 0.0062331873 
     800    18.219225    3032.4162    2699.8707    187.43547    332.54543    453.40674    486.16573    441.12346    32.847783   -437.39291    1306144.4     -1306788    1701.7675    48631.318    293.75377 0.0056528077 
     850    19.320825    2898.4936    2563.6961     177.9817    334.79757    463.66634    486.19928    453.38802    34.062236   -455.86081    1306144.2   -1306790.9   -285.04073    48631.318    278.93762 0.0052778244 
     900     20.41979    2780.3551    2528.3241    175.52604    252.03099    396.92693     451.7645    435.59756    33.035261   -413.46181    1306142.9   -1306794.7    3836.4347    48631.318    275.08801 0.0070307677 
     950    21.517533    2679.3418    2456.8821    170.56626    222.45967    385.66649     434.6516    418.37957    32.156706   -387.22039    1306136.9   -1306798.1    5510.2277    48631.318    267.31518 0.0064041284 
    1000    22.614275     2593.435    2367.4471    164.35734    225.98798    427.85237    453.27432    415.48822    31.097611   -436.61808    1306131.8   -1306796.9    1166.3709    48631.318    257.58457 0.0059160188 
    1050    23.688642    2524.7784    2305.0257     160.0238    219.75264    432.90797     438.8666    412.79338    30.892595   -414.29467    1306119.4   -1306800.8    1698.2602    48631.318     250.7925 0.0065595368 
    1100    24.750163     2471.818     2311.095    160.44516    160.72297    378.43554     453.3434      392.485    29.012487   -409.64322    1306119.6   -1306802.5    4190.9174    48631.318     251.4532 0.0059713928 
    1150    25.813605    2433.9311    2279.0768    158.22233    154.85433    395.30409    436.87935    414.39367    31.118959   -428.90913    1306110.2   -1306804.2    3274.9237    48631.318    247.96895 0.0069037916 
    1200    26.876952    2411.3772    2238.4639    155.40283    172.91329    453.61525    460.27658    408.59192    31.237007   -482.78468    1306110.2   -1306808.2   -523.10237    48631.318    243.55013 0.0068752641 
    1250    27.929701    2402.1937    2286.0559    158.70685    116.13778    416.44884    462.75935    391.75448    29.446777    -477.6718    1306102.2   -1306808.8     484.0561    48631.318    248.72561  0.011679662 
    1300    29.000999    2406.5014     2261.274    156.98639    145.22737      408.678    437.74824    400.45662    30.448139   -418.44472    1306096.8   -1306810.5    4490.4105    48631.318     245.9924  0.076575975 
    1350     30.07322     2459.141    2317.5852    160.89573    141.55579    651.85736    447.40791    400.66662    29.060882   -461.45016    1305884.3   -1306810.3     693.5247    48631.318    250.14112    3.5619231 
    1400     31.14859    2479.6103    2285.6714    158.68015    193.93893    582.54135    457.54445    430.29301    30.184026   -449.49877    1305955.6   -1306812.8    930.44669    48631.318    247.21806    2.5941109 
    1450    32.226914     2498.357    2286.4857    158.73668    211.87137    434.79636    477.95951    402.79572    31.070593   -406.60139    1306086.4   -1306814.5    2933.5045    48631.318    248.74572  0.058613153 
    1500    33.410717    2546.6608    2423.6247    168.25741    123.03609    392.07322    456.01243    385.97344    29.255562   -417.91413    1306089.9   -1306812.3     3333.391    48631.318     263.6939  0.011242005 
    1550    34.466176    2596.5534    2325.2208    161.42583    271.33259    462.52172    469.54241    461.20405    34.616224   -423.51068    1306080.4   -1306813.4    2155.1194    48631.318    252.98718  0.011190963 
    1600    35.524206    2646.7837    2387.8846    165.77619     258.8991    424.60563    484.95051    449.57767    33.318683   -395.68293      1306077   -1306814.8      1291.42    48631.318    259.80456   0.01242131 
    1650    36.582854    2700.2921    2387.3119    165.73643    312.98026    431.01369    496.39909    455.52591    32.725057   -357.65832    1306070.3   -1306815.3    5006.9348    48631.318    259.70291  0.081728845 
    1700    37.641527    2777.9572    2386.7777    165.69934     391.1795    636.55763    523.11512     482.8483    35.185863    -391.0955    1305919.8   -1306815.2    2192.6733    48631.318     258.1403    2.7324891 
    1750    38.722299    2829.6167    2559.2488    177.67295    270.36793    684.60746    479.95058    446.29664    31.887359   -385.83616    1305832.5     -1306819    1683.6061    48631.318      276.955    2.6459088 
    1800    39.800548    2835.7772    2465.7031    171.17865    370.07414    470.05306    508.38361    479.70121    37.826988    -369.0694    1306062.8   -1306819.6    3022.9801    48631.318    268.22328  0.097437593 
    1850    40.878327      2857.76    2504.4099    173.86582    353.35016    436.05857    516.10495    487.70907    36.514477   -385.43957    1306078.9   -1306816.5    2950.6415    48631.318    272.48049  0.016822774 
    1900      41.9583    2867.7843    2528.8424    175.56202    338.94193    446.38058    509.30719    485.04661    37.284135   -402.67104    1306076.5   -1306812.9    3161.5835    48631.318     275.1418  0.011620333 
    1950    43.058281    2861.3388    2513.8846     174.5236    347.45414    470.99292    536.81741    467.97736    36.047648   -430.00695    1306079.3   -1306813.6    739.25154    48631.318    273.50953  0.020089235 
    2000    44.142059     2838.068    2530.3189    175.66453    307.74914    423.19157    516.85371    454.76945    35.048253   -387.49234    1306074.6   -1306809.3    4324.0966    48631.318    275.23081   0.13784772 
Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms

Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.008     | 22.592     | 23.892     |  21.7 | 51.18
Bond    | 4.8951     | 5.1338     | 5.2542     |   6.4 | 11.63
Kspace  | 9.1158     | 10.514     | 12.296     |  35.3 | 23.82
Neigh   | 0.63826    | 0.63849    | 0.63875    |   0.0 |  1.45
Comm    | 0.78008    | 0.80146    | 0.84186    |   2.7 |  1.82
Output  | 0.0036852  | 0.0040929  | 0.0052037  |   1.0 |  0.01
Modify  | 4.3966     | 4.4074     | 4.4147     |   0.3 |  9.98
Other   |            | 0.05088    |            |       |  0.12

Nlocal:    1375 ave 1415 max 1340 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost:    8101 ave 8147 max 8056 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:    326274 ave 342552 max 306832 min
Histogram: 1 0 0 0 1 0 1 0 0 1

Total # of neighbors = 1305095
Ave neighs/atom = 237.29
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:44
